Notes for batch 18957 which has some repeated samples from batch 18840.

docs/18170_run_notes.md

+# Run 18170
+
+There are 5 samples on this run that failed on run 18840, all are from different families. We’ve put the whole family into the PED file. The rest of the family’s data are on run 18840. The repeated samples on this run are:
+
+* 125778 (family 428004)
+* 125467 (family 427734)
+* 101846 (family 429213)
+* 125303 (family 427554)
+* 125783 (family 428055)
+
+Other analysis notes:
+* 430321 – Quad, 2 affected children. Please perform trio-based analysis per child, the 2 are not similarly affected.
+* 429107 – Quad, 2 similarly affected children. Please perform shared variant analysis between 88303 and 80901, and trio-based analysis per child.
+* 429453 – Trio, mother & child similarly affected. Please perform trio-based analysis and shared variant analysis between 126602 and 126605.
+* 429187 – Duo, for Congenica analysis only.
+
+## Read set up
+
+```
+cd /scratch/u035/project/trio_whole_exome/analysis/reads
+mkdir 18170_Ansari_Morad
+cd 18170_Ansari_Morad
+
+cp ../17710_Ansari_Morad/*428004* ./
+cp ../17710_Ansari_Morad/*427734* ./
+cp ../17710_Ansari_Morad/*429213* ./
+cp ../17710_Ansari_Morad/*427554* ./
+cp ../17710_Ansari_Morad/*428055* ./
+
+ls -lh 125778_428004*
+ls -lh 125467_427734*
+ls -lh 101846_429213*
+ls -lh 125303_427554*
+ls -lh 125783_428055*
+
+rm 125778_428004*
+rm 125467_427734*
+rm 101846_429213*
+rm 125303_427554*
+rm 125783_428055*
+```
+
+## Parameter file generation
+
+```
+cd /scratch/u035/project/trio_whole_exome/analysis/params
+
+version=v1
+project_id=18170_Ansari_Morad
+sample_suffix=_WESTwist_IDT-A
+ped_file=18957_WES_PED_110621.txt 
+
+ln -s $ped_file $project_id.ped
+```
+
+Edit the parameter generation script to exit after running the Perl script for producing the PED files.
+
+```
+/home/u035/project/scripts/prepare_bcbio_config.sh \
+   /home/u035/project/scripts/trio_whole_exome_config.sh \
+   $project_id $version $sample_suffix &> ${version}_${project_id}.log
+```
+
+Copy the PED files for the above families from the previous run and edit the batch id.
+
+```
+for family in 428004 427734 429213 427554 428055
+do
+  cp 17710_Ansari_Morad_18840_${family}.ped 18170_Ansari_Morad_18957_${family}.ped
+  perl -pi -e 's/18840/18957/' 18170_Ansari_Morad_18957_${family}.ped
+done
+```
+
+Edit the parameter generation script to skip running the Perl script for producing the PED files.
+
+```
+/home/u035/project/scripts/prepare_bcbio_config.sh \
+   /home/u035/project/scripts/trio_whole_exome_config.sh \
+   $project_id $version $sample_suffix &> ${version}_${project_id}.log
+```
+
+Uncomment out the skipped section of the parameter generation script. Check config files for families.
+